LibME—automatic extraction of 3D ligand‐binding motifs for mechanistic analysis of protein–ligand recognition

Identifying conserved binding motifs is an efficient way to study protein–ligand recognition. Most 3D binding motifs only contain information from the protein side, and so motifs that combine information from both protein and ligand sides are desired. Here, we propose an algorithm called LibME (Liga...

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Bibliographic Details
Published in:FEBS open bio 2016-12, Vol.6 (12), p.1331-1340
Main Authors: He, Wei, Liang, Zhi, Teng, MaiKun, Niu, LiWen
Format: Article
Language:English
Subjects:
algorithm
Algorithms
Amino acids
binding motif
Investigations
Isocitric acid
Ligands
Method
Methods
Proteins
protein–ligand recognition
Signal transduction
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Summary:Identifying conserved binding motifs is an efficient way to study protein–ligand recognition. Most 3D binding motifs only contain information from the protein side, and so motifs that combine information from both protein and ligand sides are desired. Here, we propose an algorithm called LibME (Ligand‐binding Motif Extractor), which automatically extracts 3D binding motifs composed of the target ligand and surrounding conserved residues. We show that the motifs extracted by LibME for ATP and its analogs are highly similar to well‐known motifs reported by previous studies. The superiority of our method to handle flexible ligands was also demonstrated using isocitric acid as an example. Finally, we show that these motifs, together with their visual exhibition, permit better investigating and understanding of protein–ligand recognition process. Protein–ligand recognition is essential for many biological activities in living cell. In this manuscript, we reported a novel algorithm, LibME or Ligand‐binding Motif Extractor, which extracts biologically meaningful 3D binding motifs by taking information from both the protein and its ligand into account. A ligand‐binding motif is generated by extracting conserved residues, in terms of chemical nature and their relative locality to the ligand, from a set of proteins binding the same ligand. These extracted motifs, together with a PyMOL visualization, can be used to identify key interactions as well as their conservation in the binding of a target ligand, thus permitting better understanding of the protein–ligand recognition process.
ISSN:2211-5463
2211-5463
DOI:10.1002/2211-5463.12150